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What are the implications of building a java program against the jars of one web container (say Jetty) and running it in another (say Tomcat)?
I have an application which I run in Jetty durring development but which is deployed into a tomcat server for production (Why? because it seems easier to develop without having to run a whole tomcat server.)
You should compile against only the official Java EE API’s for the level you target, for any non-developer builds. Preferably by a build engine. Preferably on a different operating system than you develop on.
For a web application this mean the appropriate servlet API as downloaded from Oracle. Similar for an enterprise application.
In my experience this is the best way to keep it straight.
Edit: Java EE SDK is available from http://www.oracle.com/technetwork/java/javaee/downloads/index.html. If you need an older version than Java EE 6, then follow the “Previous Releases” link.